How can I adapt the packages and algorithms for SNP calling Affymetrix
chips for Fluidigm SNP chips?  I am unfamiliar with Affymetrix chips and
how they are normalized.


The data that is exportable from the fluidigm chips comes out normalized
already so I don't believe any normalization steps would be required.  I
would like a way to import the x and y data properly for each SNP and apply
the existing algorithms for calling and be able to read up on what
algorithm I'm using if it is successful.  It would be important to have an
algorithm that would be selective on calls and "no call" when appropriate.

Thank you for your help.  I've been searching and exploring different
packages and options from publications but if someone could direct me to
what they have found works well I would appreciate it greatly.

To do the work of myself I believe I will need to know what packages are
used to import the normalized data along with what functions are used and
what functions are used for the genotyping algorithm.  If I have these
things I can manipulate my data to fit it.

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